Single-cell transcriptomic characterization of a human MDS hematopoietic dataset and in vitro validation of apoptosis-related venetoclax resistance in human MDS-L cells

Abstract

Myelodysplastic syndromes (MDS) are heterogeneous clonal hematopoietic disorders in which dysregulated apoptosis, oxidative stress, and adaptive survival signaling contribute to disease persistence and therapeutic resistance. Venetoclax (VEN) targets BCL-2-dependent survival, but resistance is frequently accompanied by compensatory survival programs. Whether ferroptosis-associated transcriptional states are dynamically remodeled during VEN treatment and participate in this adaptive phenotype remains incompletely understood. We analyzed two independent human MDS single-cell RNA-sequencing cohorts together with an in vitro VEN-resistant MDS-L model. GSE241417 was used to characterize longitudinal and cell-state-specific ferroptosis-associated transcriptional patterns, whereas GSE180298 provided independent single-cell validation. Longitudinal module scores were summarized across major hematopoietic states and treatment stages. Apoptosis/proliferation- and ferroptosis-related genes were further examined by qRT-PCR in parental and VEN-resistant MDS-L cells. Single-cell analysis revealed marked heterogeneity of ferroptosis-associated transcriptional programs across MDS hematopoietic populations. Longitudinal trajectories in GSE241417 demonstrated nonuniform, treatment-stage- and cell-state-dependent remodeling of ferroptosis balance, inflammatory context, and survival-associated programs. The independent GSE180298 cohort reproduced major disease-associated ferroptosis-related transcriptional differences. In VEN-resistant MDS-L cells, MCL1 , BCL2L1 , MKI67 , GPX4 , SLC7A11 , and NFE2L2 were increased, whereas BCL2 , DDIT3 , ACSL4 , and NCOA4 were decreased, indicating coordinated adaptation of apoptotic and ferroptosis-related pathways. This study reveals cell-state-dependent and temporally dynamic ferroptosis-associated remodeling in MDS and identifies a coordinated apoptosis-redox transcriptional program associated with VEN resistance. The integration of longitudinal single-cell analysis, independent single-cell validation, and targeted qRT-PCR supports ferroptosis-defense pathways as a biologically relevant component of VEN-resistant adaptation and provides a rationale for future combination strategies that address both apoptotic dependence and redox-state plasticity.